AFAICT, when a Region FX is created in Melodyne, SONAR also passes the clip boundaries to Melodyne for the edit. I think this keeps them from "stepping on each other's toes" while they are working in tandem (ARA mode). For what you are doing, you may want to use Melodyne in stand-alone mode (at least for length edits) and then save the file with the same name (destructive edit). If open, SONAR will recognize that the file has been altered and ask you if you want to load the updated file.
In so inclined, you can also achieve the same results by adding Melodyne to the
Utilities Menu (as a wave editor), but I no longer have it included in mine so cannot test, but use Audition this way all the time. This would save the step of launching/navigating Melodyne (stand-alone) to that initial clip. Mudgel posted a nice example of what those entries look like for Sound Forge in
this post (may be easier to understand seeing that, just alter the red text to the appropriate Melodyne specific info).